libdna
bwa
| libdna | bwa | |
|---|---|---|
| 2 | 3 | |
| 20 | 1,454 | |
| - | - | |
| 7.4 | 2.7 | |
| 3 months ago | about 1 month ago | |
| C | C | |
| MIT License | GNU General Public License v3.0 only |
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libdna
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A good, fast hash for nucleotides triplet converted to 0, 1, 3, 2 using `3 & (nuc << 1)`
While that works for the canonical bases your method won't support CCN which should give Proline. Hence, for my implementation I have opted for a slower but more general approach. As protein coding sequences are usually short performance isn't an issue, really.
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Counting the number of matching characters in two ASCII strings
In Bioinformatics, if you now the number of mismatching characters between two strings of DNA your can compute their evolutionary distance. As DNA is long, easily a few megabytes, computing such a hamming distance via SIMD really pays of. Here is my implementation if anyone is interested: https://github.com/kloetzl/libdna
bwa
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my friend showed me his code, thees are all functions
Check out these sweet macros (from the same repo): https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/kbtree.h
- Scientists Are Finding Fungi in Cancerous Tumors
- Burrows–Wheeler Transform
What are some alternatives?
samtools - [Moved to: https://github.com/ingolia/SamTools]
foldseek - Foldseek enables fast and sensitive comparisons of large structure sets.
htslib - C library for high-throughput sequencing data formats
slivar - genetic variant expressions, annotation, and filtering for great good.
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
pn2codon - Python Rust FFI for reverse-translating Amino Acid sequences to DNA sequences
sra-tools - SRA Tools
ProteinToCodonTranslator
bowtie - An ultrafast memory-efficient short read aligner
spades - SPAdes Genome Assembler
libBigWig - A C library for handling bigWig files